Sparky - going to have a stab and answering your question as I see it but will probably talk rubbish. 
Prejudice and discrimination ultimately come from fear. Fear comes from the ego. Whether our ego is teh result of conditioning or instinct or both, I don't know. Probably a bit of both. But everything we believe about ourselves and everything around us is a judgement, no more or less. Our collective judgements may be that this is a man and that is a cat and this is a tree which helps us to operate in a way which makes sense of teh world around us.
The problems come when we apply secondary judgements. So we get 'superior man', 'common man', 'working man', lazy man', 'powerful man' and so on (or women, religion, society, race, whatever). If you look at any of these and you don't fit with it, you may react through fear because your ego feel threatened, so at best you avoid it. Fear something enough and you want to subjugate it, or obliterate it.
Religion - well, as a former Christian I've never actually come across being told to kill someone and have never been through the Catholic/Protestand polarisation as exists in Northern Ireland. But I have seen the scorn poured on the Anglo-Catholics by the Envangelicals and vice versa, and the sheer loathing of the 'traditionalists' (i.e. anti-gay) have for the liberlas and reformers, to the point where the church splinters and fractures and teh in-fighting and political manouverimng makes Westminster grown-up. Everything was about division and separation which is why I walked out, first on organised religion and then on religion altogther, because instead of uniting me with my fellow sisters and brothers it divided me from them.
I suspect that somewhere down teh line we've been conditioned to be prejudiced to the point where it is instinctive - as happened with the Holocaust, European Christians had been taught to make Jews the scapegotas for centuries.
Xenia, my mum became the first female partner at the international (and very well-known) firm where she worked before setting up on her own. By doing so she opened the way for other female partners. She never felt she had to be ruthless or adopt male values to succeed, just be brilliant at what she does. Her being made partner changed the culture in her firm; sometimes one woman achieving for herself changes how women are regarded on a much wider scale.